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Secret Arts Monk [3.5 homebrew]

This is a homebrew variant of the 3.5 monk I've been working at in my spare time over the past year or so, but only just recently got refined to the point where I figure it's ready to put up for public evaluation. I know I'm hardly the first to try to fix the monk, but I came up with a way of approaching it that I thought captured the flavor of the class quite nicely and decided to try to flesh it out into something playable.

Primarily, I was looking for a way to fix the monk's class features while more or less preserving their core identity. I really want to like the RAW monk's class features -- they're very interesting and flavorful, but the fact is that they're pretty lackluster. There's essentially no synergy between them, and most of them are pretty lackluster. A lot of the ones that could be useful (like the adamantine ki strike or tongue of the sun and moon) come way too late to really be noteworthy.

The core of my idea is a system of modular class features, choosing from a list of "secret arts" and "sublime arts" (preserving the mystical kung-fu master flavor). Many of these are based on the monk's existing class features, but I've also added several of my own devising that seemed interesting, useful, and/or thematically appropriate. Secret arts are gained early on, and start out simple and modest but are improved with level. Sublime arts are essentially all of the class features the regular monk would gain after level 10, with a few modifications and additional options; these do not improve. The modular nature of the system should allow players to select a set of class features that synergize well to fit any of several different concepts, and also help to support the notion of a variety of different martial arts traditions a monk might choose from. Several of the secret arts are intended to help mitigate MAD by boosting areas that tend to fall behind -- for example, the first rank of the wholeness of body secret art helps make up for a mediocre Con score by adding additional bonus HP from Wis.

I also tweaked several other areas: The BAB and hit die for the class are now more appropriate for a mainline combatant class. The AC bonus is slightly accelerated. I've cribbed heavily from Pathfinder's ki pool system for the monk, which I feel is a good way of handling the monk's supernatural abilities. I also took inspiration from Pathfinder in expanding the flexibility in bonus feats and giving Stunning Fist as a default bonus feat right off the bat -- because let's be honest, who doesn't take Stunning Fist as their first-level bonus feat? And there are a few other smaller tweaks that you'll find in the descriptions below.

I'm shooting for a power level roughly on par with the ToB classes, mainly so that this variant monk can be a competitive alternative to the unarmed swordsage for someone who wants to play a kung-fu style character and doesn't find the swordsage quite to their liking. Let me know if I've succeeded -- and if not, where I went wrong!

Alignment: Any. While a monk's training requires intense personal discipline and dedication, which are often seen as lawful traits, there are many different paths and traditions to choose from. Any individual of any alignment can find a school of thought to suit their own personal inclinations. The one trait that all monks truly share is that they are philosophical -- not mere thugs skilled in brawling, but rather seekers of enlightenment who refine themselves, mind, body, and soul, in search of sublime transcendence. A lawful monk may seek enlightenment by following strict teachings handed down through the generations in an established temple, whereas a chaotic monk may puruse an esoteric path of individual self-discovery. A good monk may see compassion and self-sacrifice as crucial steps on the path to enlightenment, whereas an evil monk may see them as weaknesses to be overcome. A neutral monk may seek to strike a balance between dangerous extremes. Whatever your alignment, try to come up with a general philosophy of enlightenment to go with it, and use that to color your roleplaying.

Kama, nunchaku, quarterstaff, sai, shuriken, and siangham are considered special monk weapons, and can be used in a flurry of blows and for certain other class features.

Monks are not proficient with any armor or shields

When wearing armor, using a shield, or carrying a medium or heavy load, a monk loses her AC bonus, as well as her fast movement and flurry of blows abilities.

Unarmed strike
-------------------
Same as the regular 3.5 monk.

AC bonus (Ex)
------------------
When unarmored and unencumbered, the monk adds her Wisdom bonus (if any) to her AC. In addition, a monk gains a +1 bonus to AC at 1st level. This bonus increases by 1 at 4th level and every four monk levels thereafter (+2 at 4th, +3 at 8th, +4 at 12th, +5 at 15th, and +6 at 20th).
These bonuses to AC apply even against touch attacks or when the monk is flat-footed. She loses these bonuses when she is immobilized or helpless, when she wears any armor, when she carries a shield, or when she carries more than a light load.

Flurry of blows (Ex)
----------------------
Same as the regular 3.5 monk.

Improved flurry

When a monk reaches 5th level, the penalty to attack rolls when using a flurry of blows is reduced by 1, to -1 on all attacks. At 9th level, the penalty disappears entirely.

Greater flurry

When a monk reaches 11th level, her flurry of blows ability improves. In addition to the standard single extra attack she gets from flurry of blows, she gets a second extra attack at her full base attack bonus.

Bonus feats
-------------
At 1st level, the monk gains Stunning Fist as a bonus feat, and may select an additional bonus feat from the following list. The monk gains an additional bonus feat from this list at 2nd level and again at 6th level. A monk need not have any of the prerequisites normally required for these feats to select them.

At the DM's option, this list may be expanded with additional appropriate feats from other sourcebooks that will be permitted for use in the campaign.

Evasion (Ex)
---------------
Same as the regular 3.5 monk, and likewise with improved evasion.

Fast movement (Ex)
-------------------------
Beginning at 3rd level, a monk gains an enhancement bonus to speed as long as she wears no armor and carries no more than a light load. This bonus starts at +10 ft at 3rd level, and improves by 10 ft at 6th level and every three levels thereafter, as shown on the table.

Secret arts
-------------
At 3rd, 4th, and 7th level, a monk learns a secret art -- a special technique discovered on his path to enlightenment. Each secret art provides a special ability that can be improved through further training. Each secret art has five ranks (Initiate, Disciple, Master, Grandmaster, and Perfected), with each rank providing a greater benefit. A secret art is learned at Initiate rank, and a monk can improve her rank in a secret art at 6th level and at each even-numbered level thereafter. A monk cannot advance past the rank of Grandmaster in any art except at 20th level or above.

Perfected art
At 20th level, a monk can choose to Perfect a single secret art in which she has already attained the rank of Grandmaster. This is the only time that a monk can advance beyond Grandmaster rank in an art. If the monk does not wish to Perfect an art, or has not attained Grandmaster rank in any art (and thus cannot Perfect the art), she instead may simply improve an art as normal.

Ki pool (Su)
--------------
Beginning at 4th level, a monk gains access to a store of inner power called ki, which can be used to enable extraordinary feats. The monk gains a number of ki points per day equal to 1/2 her monk level + her Wis modifier, and can spend a ki point as a swift action to gain one of the following benefits until the beginning of her next turn:

Enhancement bonus to attack and damage with unarmed strikes equal to +1 per 4 monk levels, to a maximum of +5 at level 20

+4 dodge bonus to AC

+20 ft bonus to movement speed

Make an additional stunning fist attempt in a round, which doesn't count against your usual uses per day of that ability.

Ki Strike (Su)
----------------
Beginning at 4th level, as long as the monk has at least 1 point remaining in her ki pool, her unarmed strikes are infused with ki. This causes the monk's unarmed strikes to be considered magic for the purposes of overcoming damage reduction and being able to hit incorporeal creatures.

Improved ki strike
At 10th level and again at 16th level, the monk gains an improvement to her ki strike, gaining an additional benefit from the following list as long as at least 1 ki point remains in her ki pool.

Adamantine strike: The monk's unarmed strike is considered adamantine for the purposes of overcoming DR and hardness.

Uncanny strike: Any time the monk would suffer a miss chance on attacks against an opponent due to concealment or a similar effect (such as the Blur or Displacement spells), the miss chance is reduced by half.

Axiomatic strike: The monk's unarmed strike becomes lawful-aligned for overcoming DR. Only a lawful monk may select this option.

Holy strike: The monk's unarmed strike becomes good-aligned for overcoming DR. Only a good monk may select this option.

Unholy strike: The monk's unarmed strike becomes evil-aligned for overcoming DR. Only an evil monk may select this option.

Balancing strike: The monk gains a +5 bonus on damage rolls when making an unarmed strike against a lawful good, chaotic good, lawful evil, or chaotic evil opponent whose damage reduction is effective against her unarmed strikes. This benefit does not apply against a target if its alignment is not among those listed, it does not have damage reduction, or its damage reduction does not apply to your attacks. For example, a monk with adamantine strike as well as this benefit would not gain a bonus to damage rolls against creatures with DR overcome by adamantine weapons. Only a true neutral monk may select this option.

Purity of Body (Su)
---------------------
At 5th level, a monk gains immunity to all diseases, including supernatural and magical diseases.

Diamond Body (Su)
----------------------
Same as the regular 3.5 monk.

Sublime Arts
----------------
At 12th level, and again at 13th level and every odd-numbered level thereafter, a monk learns a sublime art. Like secret arts, sublime arts are special abilities a monk learns as part of her training; however, unlike secret arts, sublime arts cannot be improved by further training. A monk chooses her sublime arts from the following options:

Abundant Step (Su): As a move action, the monk may spend 2 ki to slip between spaces as though using the Dimension Door spell with a caster level equal to her monk level. The monk can only transport herself and carried objects up to her heavy load in this way.

Quivering Palm (Su): The monk can set up vibrations within the body of another creature that can thereafter be fatal if the monk so desires. The monk must declare she is using this ability before making an unarmed attack. If the attack misses, the attempt is wasted; if it hits, the monk can then will that creature to die as a free action at any time within the next week. At this time, the target must make a Fort save (DC 10 + 1/2 monk level + Wis bonus) or die immediately. On a successful save, the target instead takes 1d6 damage per point of Wis bonus the monk has (minimum 1d6). This ability does not affect creatures that are immune to critical hits, and a monk can only have one quivering palm effect active at once. If the monk uses this ability while another is in effect, the previous effect is negated. This ability can be used a number of times per day equal to the monk's Wis bonus (minimum once per day). Only a monk of 15th level or higher can learn this sublime art.

Tongue of the Sun and Moon (Ex): The monk can speak with any living creature.

Empty Body (Su): As a move action, the monk can spend 3 ki to become ethereal for 1 minute, as though using the spell Etherealness. This ability cannot be used to make any other creature ethereal. Only a monk of 15th level or higher can learn this sublime art.

Summer's Burning Fury (Su): The monk gains resistance 20 to fire, and can spend 2 ki as a standard action to shroud herself in an aura of fire for 1 round per monk level or until the aura is discharged. This aura deals fire damage equal to the monk's level + her Wis bonus to any creature that attacks the monk with a natural or non-reach manufactured melee weapon, and causes her unarmed strikes and special monk weapon attacks to deal bonus fire damage equal to her Wis bonus. The monk can discharge this aura as a swift action to produce a 60-ft cone-shaped burst of flame, dealing 10d6 fire damage and dazing all affected creatures for 1 round. A successful Ref save (DC 10 + 1/2 level + Wis bonus) halves the damage and negates the dazing effect.

Winter's Frigid Scorn (Su): This sublime art functions as Summer's Burning Fury, except that the resistance and damage type is changed to cold and the discharge entangles instead of dazes.

Spring's Stormy Passion (Su): This sublime art functions as Summer's Burning Fury, except that the resistance and damage type is changed to electricity and the discharge blinds instead of dazes.

Autumn's Bitter Disdain (Su): This sublime art functions as Summer's Burning Fury, except that the resistance and damage type is changed to acid and the discharge sickens instead of dazes.

Shadow of the Moon (Su): As long as the monk has at least 1 point of ki available, she can fade into shadows as a standard action, gaining total concealment as long as she remains within an area of less than bright illumination. This effect lasts until the monk dismisses it (a free action), enters a brightly illuminated area, or runs out of ki.

Light of the Sun (Su): As long as the monk has at least 1 point of ki available, she can produce light as a free action. This ability can produce bright light to a maximum radius of 10 ft x the monk's Wis bonus, but the monk can freely control the brightness and radius. Additionally, the monk can spend 2 ki as a standard action to intensify this light to blinding brightness in a radius of 10 ft x her Wis bonus for 1 round per level. Each sighted creature within range must make a Fort save (DC 10 + 1/2 level + Wis bonus) or be blinded for the duration of the effect. A creature that makes its save is instead dazzled, but is otherwise not further affected unless it attacks the monk. A creature that attacks the monk or targets her with an effect requiring line of sight while within the radius of this effect must make another Fort save of be blinded for the remainder of the effect's duration. A creature can attempt to avert its eyes (a free action) to gain a 50% chance to avoid needing to attempt a save, but doing so imparts a 20% miss chance to its attacks against the monk and a 20% failure chance for its spells and effects targeting the monk that require line of sight. This effect suppresses all darkness spells and effects within its radius with a level less than or equal to 1/2 the monk's level.

Secret Art: In place of learning a sublime art, the monk can learn a new secret art at initiate rank.

Improved Art: In place of learning a sublime art, the monk can improve her rank in a secret art she knows.

Perfect Self
--------------
As the regular 3.5 monk, except the DR is overcome by a single alignment opposite that of the monk's own alignment on one axis. For example, a lawful good monk can gain DR 10/evil or DR 10/chaotic. A true neutral monk may choose any single alignment to overcome her DR. This choice cannot be changed once made.

=============== Secret Arts
===============

Still Mind (Ex)
-----------------------
The monk focuses her thoughts to resist outside influence, improve her perception, and enhance her use of ki.

Initiate: The monk gains a +2 bonus to saves against mind-affecting effects and the size of her ki pool is increased by two.

Disciple: the monk's bonus to saves improves to +3, and she adds her Wis bonus to initiative checks. Furthermore, the save DCs of all Wis-based extraordinary and supernatural abilities she has are increased by 2.

Master: The monk's bonus to saves improves to +4, and she gains the uncanny dodge and improved uncanny dodge class features. Additionally, the monk can meditate for a half hour once per day to recover ki points and remove fatigue and exhaustion as though she had rested for 8 hours. This meditation also satiates the monk's stomach, allowing her to go without food as long as she meditates daily. However, this meditation cannot duplicate the other benefits of rest, such as natural healing and the ability to prepare new spells or recover spell slots.

Grandmaster: The monk gains blindsense to a range of 10 ft x her Wis bonus. This ability is not dependent on any single sense, and functions even when the monk is deaf or in an area of magical silence. Additionally, as a standard action, the monk can spend 2 ki to gain the benefits of the True Seeing spell for 1 minute per level.

Perfected: The monk's blindsense improves to blindsight, and she gains immunity to all mind-affecting effects. Furthermore, she can now activate the True Seeing ability granted by this secret art as a swift action.

Petals of Wind (Su)
-------------------------
The monk uses her ki to control air currents to her advantage.

Initiate: The monk gains a +10 bonus to Jump checks. She also can cause a cushion of air to slow falls, reducing the effective distance fallen when determining falling damage by 5 ft per monk level.

Disciple: The monk's bonus to Jump checks improves to +20. Additionally, as long as she has at least one point of ki in her ki pool, she can shroud herself in a mantle of winds, causing all normal ranged weapons to gain a 30% miss chance against her. This ability can be turned on or off as a swift action, and can be used for a total number of minutes per day equal to her monk level. She can divide this duration however she likes, as long as the total duration does not exceed her monk level in minutes per day.

Master: The monk's bonus to Jump checks improves to +30. Additionally, she may spend 1 ki point as a swift action to attack with blasts of air, treating her unarmed strikes as thrown weapons with a maximum range of her natural reach + 25 ft for 1 round.

Grandmaster: The monk gains the ability to fly at her land speed (including fast movement bonus) with good maneuverability for a number of rounds per day equal to twice her monk level + her Wis bonus. She may activate or deactivate this ability as a free action and divide the duration as she chooses throughout the day, but cannot use it unless she has at least one point of ki in her ki pool.

Perfected: The monk no longer has any limitations on the duration of her flight and mantle of winds ability. She can keep them on permanently if she so desires.

Wholeness of Body (Su)
----------------------------
The monk uses her ki to heal wounds and resist injury.

Initiate: The monk adds her Wis bonus to the HP gained for each monk level in addition to her Con bonus. This applies retroactively to monk levels taken before learning this secret art, but the monk does not gain additional HP for levels taken in other classes.

Disciple: The monk can spend 2 ki as a move action to heal an amount of HP equal to twice her monk level + her Wis bonus.

Master: The monk adds her Wis bonus to Fort saves. Additionally, she can spend 2 ki as a standard action to cure an amount of ability damage to each of her physical ability scores equal to her Wis bonus (minimum 1), or cure that much permanent ability drain to a single one of her physical ability scores.

Grandmaster: The monk may restore HP using this ability as a swift action, and gains a 50% chance to ignore extra damage from critical hits, sneak attacks, and similar effects, as though wearing armor with the fortification property.

Flow of the River (Ex)
---------------------------
The monk learns to move like flowing water.

Initiate: The monk gains Dodge as a bonus feat, even if she doesn't meet the prerequisites. She also gains a +1 dodge bonus to AC and Ref saves during any round in which she moves at least 10 ft, and adds her Wis bonus to Tumble and Escape Artist checks.

Disciple: The monk gains Mobility as a bonus feat, even if she doesn't meet the prerequisites, and her dodge bonus during rounds in which she moves at least 10 ft improves to +2. Additionally, she may ignore a number of squares of difficult terrain each round equal to her Wis bonus (minimum 1). This allows her to take a 5-ft step into difficult terrain.

Master: The monk gains Spring Attack as a bonus feat, even if she doesn't meet the prerequisites, and her dodge bonus during rounds in which she moves at least 10 ft improves to +3. Additionally, when making a run or charge, she can make one turn of up to 90 degrees for each point of Wis bonus she has (minimum 1).

Grandmaster: The monk's dodge bonus during rounds in which she moves at least 10 ft improves to +4. Additionally, when she uses her flurry of blows ability, she may take a 5-ft step after each attack.

Perfected: The monk permanently gains the benefits of the Freedom of Movement spell and can take 10 on Tumble checks even in situations that would normally prohibit taking 10 on a skill check. Additionally, she may spend 2 ki as an immediate action to move up to 10 ft per point of Wis bonus (minimum 10 ft). This movement provokes attacks of opportunity as normal, but the monk can Tumble as normal (including halving halving her speed) to avoid provoking AoO.

Fury of the Storm (Ex)
-------------------------
The monk strikes with the ferocity of a raging typhoon.

Initiate: The monk adds her Wis bonus to attack and damage rolls with special monk weapons and unarmed strikes.

Disciple: The monk may use her flurry of blows ability to gain additional attacks on any attack action, not just full attacks. Additionally, she may spend 1 point of ki as a swift action to gain an addtional attack at her highest BAB in a flurry of blows.

Master: The monk may spend a point of ki as a swift action to make a full attack (including flurry of blows, if so desired) as part of a charge.

Grandmaster: The monk can now make full attacks as part of a charge without spending ki or a swift action. Furthermore, she may spend a point of ki as a standard action to make a number of attacks at her full BAB equal to the number of bonus attacks afforded by her flurry of blows ability against each creature within reach. These attacks must be made with unarmed strikes or special monk weapons, and are treated in all respects as a use of the monk's flurry of blows ability. However, the Disciple-rank ability of this secret art cannot be used to gain additional attacks as part of this ability.

Perfected: The monk may spend 3 ki to make a full attack (including flurry of blows, if so desired) as a swift action.

Roots of the Mountain (Su)
--------------------------------
The monk becomes an impassable barrier, unyielding as the mountain. She can use her ki to manipulate gravity, earth, and stone to impede her foes and draw on the power of the earth to strengthen herself.

Initiate: The monk gains a +5 bonus to Balance checks and opposed checks to resist trip, bull rush, and overrun attempts. Additionally, as long as she is touching the ground and hasn't moved more than 5 ft this round, she can enter a rooted stance as a swift action. While in this stance, enemies treat the area in a radius around the monk equal to her fast movement bonus as difficult terrain, provoking attacks of opportunity for entering these squares as well as leaving them. Allies are not affected by this ability. This stance ends when the monk loses contact with the ground or moves more than 5 ft in a single round, whether voluntarily or by force (as from a bull rush attack or the Telekinesis spell).

Disciple: The monk's bonus to checks improves to +10, and she gains DR 5/adamantine when rooted.

Master: The monk's bonus to checks improves to +15, and her rooted DR improves to 10/adamantine. Additionally, when rooted she gains a bonus to Str equal to 1/5 her fast movement bonus.

Grandmaster: The monk's bonus to checks improves to +20 and her rooted DR improves to 15/adamantine. Additionally, when rooted she can spend 2 ki as a standard action to force all creatures within a radius equal to her fast movement bonus to the ground. Each affected creature must make a Fort save (DC 10 + 1/2 HD + Wis), falling to the ground prone if they fail their save. Flying creatures are also affected by this ability, and also lose their ability to fly for a number of rounds equal to the monk's Wis bonus (minimum 1 rd) if they fail the save.

Perfected: The monk's bonus to checks improves to +30, and her rooted DR to 30/adamantine. Additionally, when entering a rooted stance, she can spend 1 ki as a free action to increase in size. She can grow up to two size categories, to a maximum size of Colossal. Her height doubles (if growing by one size category) or quadruples (if growing two categories), and her weight increases by a factor of 8 (if growing one size category) or 16 (if growing two size categories). For each size category grown, she gains a +2 size bonus to Str, a -2 size penalty to Dex (to a minimum effective Dex score of 1), and a -1 size penalty to attack rolls and AC. Her space and reach change to suit that of a creature of her new stature (10 ft space and reach for a Large humanoid, 15 ft space and reach for a Huge humanoid; see the DMG for other sizes). Her worn and carried items grow with her, and her wielded weapons (including unarmed strikes) deal more damage appropriate to their new size (see DMG p. 28); however, any enlarged item that leaves her possession (including thrown weapons) return to their original size immediately. If insufficient room is available for the desired growth, the monk attains the maximum possible size and may make a Str check to burst any enclosures in the process. If she fails, she is constrained without harm by the materials enclosing her. This effect does not stack with other size-increasing effects, such as the Enlarge Person spell. It ends when the monk dismisses it (a free action) or leaves the rooted stance.

All good saved, I fully understand where you are coming from, a monk is swift, strong and has a powerful mind; but this is unbalanced

An alternative is a high will save, and as a ki ability to let them use that save instead of fortitude or reflex equal to their monk level divided by two per day.

This preserves the flavour, but stops the mechanical a bit unfair idea.

Just to clarify -- are you saying that all strong saves in general is too strong, or more specifically in this case with the rest of the class features it gets, it makes it too strong?

Because the original monk class does have all strong saves, hence why I gave the upgrade all strong saves. And while all strong saves is definitely nice, it certainly doesn't exactly help keep the original version from being the weakest core class.
And it's not unique to monks, either -- off the top of my head, I know the favored soul gets all strong saves too, and they get full spellcasting on top of that.

A lovely take on the Monk, all in all. However, some points of criticism concerning design and game balance:

1. The design is a bit clumsy. You have uses-per-day abilities and you have a ki pool. You have secret arts and you have sublime arts. You have a huge number of class features all in all, and it will be very easy to lose track of abilities that don't come into play that often. I'd appreciate more streamlining. For example, basing all use-restricted powers on the ki pool, but increasing the pool's size or introducing a recharge mechanism, might be a good idea (à la Pathfinder). You can also grant certain passive powers whenever at least [such-and-such-many] points remain in the ki pool.

Furthermore, some abilities take only free actions to use - something which I'm always a bit leery about.

Finally, some abilities use non-standard mechanisms or calculations: halved miss chances (instead of re-rolls), miss chances of 30% etc. This just feels a bit out of sync with the rest of D&D.

2. Balance-wise, the all-good saves aren't the problem. The problem is rather that this Monk version leaves the Fighter, Ranger, Barbarian and Paladin in the dust where versatility and in some cases sheer basic combat power are concerned. It's the combination that's rather a bit too good.

A 4th level Monk with the Wholeness of Body and Fury of the Storms secret arts gets Wis to AC, HP, attack and damage. That's almost ridiculous SAD, right there. Since he also gets the regular modifiers (from Dex, Con, and Str respectively), that makes him much more powerful than the other warrior types. I don't have a problem with power, if it comes at the cost of versatility, and vice versa. But in this case, you've overdone it a little by giving the Monk both (at least where combat is called for - outside of combat, he's still not that useful).

You might want to decide whether you aim more for sheer power or great versatility. Large passive bonuses to important combat stats, especially bonuses that are based on an ability score instead of being static, should be introduced only sparingly and with good reason.

An offender of a different type is the Roots of the Mountain initiate power: It makes Enlarged, Spiked Chain-wielding Thicket of Blades Crusaders cry themselves to sleep. Potentially at 3rd level. At will, all the time. And it doesn't even cost ki. Furthermore, compared to the boost the initiate power already grants you, the improvements on the power don't really do that much, so this is a classic dip candidate. I'd totally dip Monk 3 just for this power!

So them's my thoughts on the rebuild. I really like how you specifically adressed some of the more severe shortcomings of the 3.5 and Pathfinder Monk versions. I just think you're not finished yet. Keep up the good work!

A lovely take on the Monk, all in all. However, some points of criticism concerning design and game balance:

1. The design is a bit clumsy. You have uses-per-day abilities and you have a ki pool. You have secret arts and you have sublime arts. You have a huge number of class features all in all, and it will be very easy to lose track of abilities that don't come into play that often. I'd appreciate more streamlining. For example, basing all use-restricted powers on the ki pool, but increasing the pool's size or introducing a recharge mechanism, might be a good idea (à la Pathfinder). You can also grant certain passive powers whenever at least [such-and-such-many] points remain in the ki pool.

A good point. I'll work on trying to make ki a bit more of a unifying factor for the abilities.
I do think I'll keep the secret/sublime arts division, though -- the main point there is that secret arts replace the really pathetically lackluster class features from the first ten levels (namely slow fall, still mind, and wholeness of body) with stuff that gets better as you go (and as a matter of fact, the improvements to your secret arts come when the regular monk would gain improvements to slow fall). Conversely, sublime arts replace the stuff you get in the latter ten levels of the original class, several of which would be reasonably decent as-is if only you could take them earlier (a prime example of this would be Tongue of the Sun and Moon).
As for number of class features, I don't feel that's a problem personally. It certainly has a lot of complexity compared to other core martial classes, but it's about standard compared to ToB classes (my goal/benchmark), and much less compared to full spellcasters (which I'm trying to avoid matching). By my count, a level 20 secret arts monk has 32 class features, counting each bonus feat and each rank in a secret art as a separate class feature. A warblade 20 has 28 class features if you count each stance and maneuver as an individual class feature, and the swordsage has 42! If you count individual spells as class features for spellcasters, a 20th-level sorcerer has 44 class features (more if they take a PrC of some sort), and prepared spellcasters have even more.

Furthermore, some abilities take only free actions to use - something which I'm always a bit leery about.

These I can explain. There are only four things that take free actions: The activation of a successful Quivering Palm, the regular light from Light of the Sun, the flight from grandmaster Petals of Wind, and the growth from perfected Roots of the Mountain.
Quivering Palm is a free action to trigger in its original form.
The light I felt would be fine to give as a free action, given that it's a pretty minor utility effect that you can only get at level 12, at the earliest.
The flight is essentially intended to be "you gain a fly speed, but can only use it for a certain duration per day". Not sure if that helps or not, but that was my reasoning behind making it a free action, anyway.
And finally, the growth from Roots of the Mountain isn't technically a free action at all, because it's an add-on to entering your stance. It's essentially an added benefit you get from the stance if you choose that as your capstone, but you don't necessarily have to use it.

Finally, some abilities use non-standard mechanisms or calculations: halved miss chances (instead of re-rolls), miss chances of 30% etc. This just feels a bit out of sync with the rest of D&D.

The 30% miss chance from disciple Petals of Wind I actually cribbed from the effect Wind Wall has on sling bullets and thrown weapons. It's essentially a somewhat weaker, personal Wind Wall. I have no excuse for the halved miss chance bit, though.

2. Balance-wise, the all-good saves aren't the problem. The problem is rather that this Monk version leaves the Fighter, Ranger, Barbarian and Paladin in the dust where versatility and in some cases sheer basic combat power are concerned. It's the combination that's rather a bit too good.

A 4th level Monk with the Wholeness of Body and Fury of the Storms secret arts gets Wis to AC, HP, attack and damage. That's almost ridiculous SAD, right there. Since he also gets the regular modifiers (from Dex, Con, and Str respectively), that makes him much more powerful than the other warrior types. I don't have a problem with power, if it comes at the cost of versatility, and vice versa. But in this case, you've overdone it a little by giving the Monk both (at least where combat is called for - outside of combat, he's still not that useful).

You might want to decide whether you aim more for sheer power or great versatility. Large passive bonuses to important combat stats, especially bonuses that are based on an ability score instead of being static, should be introduced only sparingly and with good reason.

An offender of a different type is the Roots of the Mountain initiate power: It makes Enlarged, Spiked Chain-wielding Thicket of Blades Crusaders cry themselves to sleep. Potentially at 3rd level. At will, all the time. And it doesn't even cost ki. Furthermore, compared to the boost the initiate power already grants you, the improvements on the power don't really do that much, so this is a classic dip candidate. I'd totally dip Monk 3 just for this power!

I'm totally fine with blowing the other PHB martial classes out of the water, since I feel they all could use a boost; the monk is just the worst offender, and the one that saddens me the most because of the unique flavor.
However, I do think you make some good points about the SAD and Roots of the Mountain ability. I was actually a little uncertain about the Wis-to-X abilities myself, but decided to leave them in because they struck me as the most appropriate way to mitigate the monk's MAD. However, I suppose I may have gone a bit too far in that regard.
As for the Roots of the Mountain ability, I'll admit that was a bit of an oversight on my part. Originally, the initiate-rank ability was DR 5/adamantine while in the rooted stance, and the difficult-terrain effect came later (either disciple or master, I don't recall which). I then realized that making DR available that early would make a low-level monk absurdly tough (albeit at the cost of mobility), so I rearranged things a little. I guess I didn't think too hard about the fact that what I was moving to initiate rank was every bit as overpowered, if not moreso!

So them's my thoughts on the rebuild. I really like how you specifically adressed some of the more severe shortcomings of the 3.5 and Pathfinder Monk versions. I just think you're not finished yet. Keep up the good work!

About the thing of Wis-to-X ability you should work more. Not that this is broken, far from that. The base line should be the existent Mod-to X ability that you encounter among the books of WotC, for example:

1- Swordsage - gain Wis to AC at lv2; Wis to chosen group of weakons damage at lv 4. But they gain medium BAB...

2- Wizard/Sorcerer - with the 4th level spell Thunderlance they can switch Str for INT/CHA in attack AND damage at lv7 (8 if you're a poor sorcerer) for some rounds per cast, that limits for rounds per day. Additionally, they get reach of 20ft and a dispel effect against force effects. But they get poor BAB...

3- Feats - there are feats that switch STR for DEX in attack. Another trade STR for DEX in damage. Taking the two feats you have DEX for attack, damage, AC and Reflex Saves. The trade off should be equivalent of two feats.

4- Magic Items - I think slippers of battle dancer grant the possibility to who has perform skill to trade Str for CHA at attack and damage. There are material components that grant weapon finesse. Take a look at the cost of such items.

5- Factotum - this one can add INT to everything. no comments on that HA.

I'm not good at balancing things, so pointing that there are other classes that can do the things you posted while giving up other things is all I can help